Related papers: Finding low-complexity DNA sequences with longdust

We present algorithms for length-constrained maximum sum segment and maximum density segment problems, in particular, and the problem of finding length-constrained heaviest segments, in general, for a sequence of real numbers. Given a…

The problem of finding aperiodic low auto-correlation binary sequences (LABS) presents a significant computational challenge, particularly as the sequence length increases. Such sequences have important applications in communication…

Clustering is an essential data mining tool for analyzing and grouping similar objects. In big data applications, however, many clustering algorithms are infeasible due to their high memory requirements and/or unfavorable runtime…

We introduce a method to estimate the complexity function of symbolic dynamical systems from a finite sequence of symbols. We test such complexity estimator on several symbolic dynamical systems whose complexity functions are known exactly.…

Data complexity is an important concept in the natural sciences and related areas, but lacks a rigorous and computable definition. In this paper, we focus on a particular sense of complexity that is high if the data is structured in a way…

String edit distances have been used for decades in applications ranging from spelling correction and web search suggestions to DNA analysis. Most string edit distances are variations of the Levenshtein distance and consider only…

High-dimensional datasets often contain multiple meaningful clusterings in different subspaces. For example, objects can be clustered either by color, weight, or size, revealing different interpretations of the given dataset. A variety of…

This paper addresses the Restricted Longest Common Subsequence (RLCS) problem, an extension of the well-known Longest Common Subsequence (LCS) problem. This problem has significant applications in bioinformatics, particularly for…

Computer-aided diagnosis system for diffuse lung diseases (DLDs) is necessary for the objective assessment of the lung diseases. In this paper, we develop semantic segmentation model for 5 kinds of DLDs. DLDs considered in this work are…

Calculating the length of a longest common subsequence (LCS) of two strings $A$ and $B$ of length $n$ and $m$ is a classic research topic, with many worst-case oriented results known. We present two algorithms for LCS length calculation…

Large language models (LLMs) often struggle to accurately read and comprehend extremely long texts. Current methods for improvement typically rely on splitting long contexts into fixed-length chunks. However, fixed truncation risks…

The existing biclustering algorithms for finding feature relation based biclusters often depend on assumptions like monotonicity or linearity. Though a few algorithms overcome this problem by using density-based methods, they tend to miss…

Laser degradation analysis is a crucial process for the enhancement of laser reliability. Here, we propose a data-driven fault detection approach based on Long Short-Term Memory (LSTM) recurrent neural networks to detect the different laser…

Working with exhaustive search on large dataset is infeasible for several reasons. Recently, developed techniques that made pattern set mining feasible by a general solver with long execution time that supports heuristic search and are…

The ability to identify interesting and repetitive substructures is an essential component to discovering knowledge in structural data. We describe a new version of our SUBDUE substructure discovery system based on the minimum description…

Adapting large language models (LLMs) to specific domains often faces a critical bottleneck: the scarcity of high-quality, human-curated data. While large volumes of unchecked data are readily available, indiscriminately using them for…

The Shortest Common Superstring (SCS) problem is a fundamental task in sequence analysis. In genome assembly, however, the double-stranded nature of DNA implies that each fragment may occur either in its original orientation or as its…

In this article, we review existing probabilistic models for modeling abundance of fixed-length strings (k-mers) in DNA sequencing data. These models capture dependence of the abundance on various phenomena, such as the size and repeat…

Computational complexity is a key limitation of genomic analyses. Thus, over the last 30 years, researchers have proposed numerous fast heuristic methods that provide computational relief. Comparing genomic sequences is one of the most…

In this paper we define a new problem, motivated by computational biology, $LCSk$ aiming at finding the maximal number of $k$ length $substrings$, matching in both input strings while preserving their order of appearance. The traditional…